constellation (version 0.2.0)

constellate: Identify when a constellation of events occur

Description

A function that reads in multiple time series data frames and calculates instances when a constellation of events occur. The user must specify the number of hours over which each event must take place, a variable to use to join the tables, and the time stamp variable. The timestamps variable in every data frame must be POSIXct class. In addition, the user must specify the event name and whether to keep all instances that events occur, or only the first or last instance. This function can ingest an arbitrary number of data frames with longitudinal time series data.

Usage

constellate(..., window_hours, join_key, time_var, event_name, mult = c("all",
  "first", "last"))

Arguments

...

An arbitrary number of time series data frames that each include the columns 'join_key' and 'time_var'

window_hours

A single numeric or vector of numerics specifying the number of hours to search for each event. The order of numerics in the vector should align with the order of data frames passed in '...'.

join_key

A string name of the column to join all time series data frames

time_var

A string name of the time stamp column in all time series data frames. The class of time_var must be POSIXct in all data frames.

event_name

A string name for events across the time series data frames

mult

A string specifying whether to return the first, last, or all instance(s) with a default value of all

Value

A data.frame, data.table with time stamps of qualifying events.

Imported functions

general data.table syntax

Errors

This function returns errors for:

• missing arguments (no arguments have defaults)

• passing an invalid mult value

• passing arguments with invalid classes (window_hours must be numeric and event_name must be a string)

• passing join_key or time_var values that are not column names in all time series data frames

• passing an invalid number of window_hours values (1 or the number of event data frames).

Examples

# NOT RUN {
library(data.table)
temp <- as.data.table(vitals[VARIABLE == "TEMPERATURE"])
pulse <- as.data.table(vitals[VARIABLE == "PULSE"])
resp <- as.data.table(vitals[VARIABLE == "RESPIRATORY_RATE"])
wbc <- as.data.table(labs[VARIABLE == "WBC"])
temp[, RECORDED_TIME := as.POSIXct(RECORDED_TIME,
  format = "%Y-%m-%dT%H:%M:%SZ", tz = "UTC")]
pulse[, RECORDED_TIME := as.POSIXct(RECORDED_TIME,
  format = "%Y-%m-%dT%H:%M:%SZ", tz = "UTC")]
resp[, RECORDED_TIME := as.POSIXct(RECORDED_TIME,
  format = "%Y-%m-%dT%H:%M:%SZ", tz = "UTC")]
wbc[, RECORDED_TIME := as.POSIXct(RECORDED_TIME,
  format = "%Y-%m-%dT%H:%M:%SZ", tz = "UTC")]

# Pass single time window for all time series data frames
# Subset first event
constellate(temp, pulse, resp, window_hours = 6, join_key = "PAT_ID",
 time_var = "RECORDED_TIME", event_name = "sirs_vitals", mult = "first")
# Pass different time window for each time series data frame
# Subset first event
constellate(temp, pulse, resp, wbc, window_hours = c(6,6,6,24),
 join_key = "PAT_ID", time_var = "RECORDED_TIME",
 event_name = "SEPSIS", mult = "first")
# Pass different time window for each time series data frame
# Identify all events
constellate(temp, pulse, resp, wbc, window_hours = c(6,6,6,24),
 join_key = "PAT_ID", time_var = "RECORDED_TIME",
 event_name = "SEPSIS", mult = "all")

# }